If you are replacing an existing deep cycle lead acid or AGM battery you can continue to use your same battery charging system and the built-in battery management system will do the rest for you. You will also notice that lithium batteries charge more efficiently than lead acid ad AGM batteries so the recovery will me much quicker.
While lead acid batteries are well understood workhorses, lithium-ion batteries are high-performance energy storage solutions that can be easily substituted without all the downsides – making them an ideal choice for replacing and upgrading worn out lead acid batteries.
The leading alternative at the moment appears to be lithium style batteries. There do not appear to be any manufacturers who are putting them in by default, but you can get hold of them... for a price. Diyelectriccar gives this diagram comparing power, cycles, availability, etc. for various different batteries:
A lead acid battery system may cost hundreds or thousands of dollars less than a similarly-sized lithium-ion setup - lithium-ion batteries currently cost anywhere from $5,000 to $15,000 including installation, and this range can go higher or lower depending on the size of system you need.
While it is normal to use 85 percent or more of a lithium-ion battery’s total capacity in a single cycle, lead acid batteries should not be discharged past roughly 50 percent, as doing so negatively impacts the battery's lifetime.
Most lithium-ion batteries are 95 percent efficient or more, meaning that 95 percent or more of the energy stored in a lithium-ion battery is actually able to be used. Conversely, lead acid batteries see efficiencies closer to 80 to 85 percent.